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Molecular Dynamics Simulation Study of Initial Protein Unfolding Induced by the Photo-Responsive Surfactants, AzoTAB
by
Chih-Ying Lin
A Dissertation Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (Chemical Engineering)
May 2014
Copyright 2014 Chih-Ying Lin

How proteins fold and unfold has been a great focus for decades. Techniques of molecular dynamics simulations provide the atomic insight of protein folding/unfolding. Proteins solvated in water remain well at the native structures under room temperature. Being perturbed by a small amount of photoresponsive surfactants, azoTAB, at room temperature, protein molecules, such as lysozyme, ribonuclease A, and α‐lactalbumin, encounter the conformational changes and partially unfold, especially in the α domain. We conduct molecular dynamics simulation in microseconds and through analysis of the structural properties of protein intermediates as functions of time, we demonstrate that the surfactant‐unfolded intermediates of protein molecules, owning the unfolded α‐domain but the relatively intact β‐domain, although the hydrophobic interaction is higher in the α domain than the β domain. The increased internal dynamics of partially‐unfolded protein molecules induced by azoTABs is potentially contributed to the increase enzymatic activity of protein. Molecular dynamics simulation has offered supporting evidence to better understand experimental phenomena.

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Molecular Dynamics Simulation Study of Initial Protein Unfolding Induced by the Photo-Responsive Surfactants, AzoTAB
by
Chih-Ying Lin
A Dissertation Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (Chemical Engineering)
May 2014
Copyright 2014 Chih-Ying Lin